AUSTRALIA'S north has been cut off from the south by savage summer weather that has torn the transcontinental rail line in two and washed Outback roads into a desert made a sea by violent floods.

Monstrous rains in the wake of collapsing Cyclone Grant yesterday derailed a giant freight train as a bridge collapsed into the Edith River in the Northern Territory, cutting the north-south rail corridor indefinitely, while sections of the Stuart Highway and other roads have been destroyed.

The Bureau of Meteorology warned the Northern Territory to expect more torrential rain as the ex-tropical cyclone Grant prepared for a comeback in the next 24 hours.

The storm is about 250km southeast of Darwin and moving southeast.

Genesee & Wyoming Australia owns the damaged Tarcoola to Darwin track as well as the train which derailed, spilling toxic copper concentrate into the Edith River.

The company said aerial assessments of the damage on Tuesday showed about 50m of track was washed away in the flooding, but a full assessment of the damage has not yet been made.

The company, which owns 5000km of track in South Australia and the Northern Territory, hauls grain, steel, gypsum, minerals, mining equipment and freight, as well as automotive and military equipment along the line it bought a year ago.

The freight train that derailed at the Edith River Crossing after flood waters washed away the tracks. Picture: Michael FranchiSource: Northern Territory News

GWA managing director Bert Easthope said it was impossible to tell how long the line, which is part of the nation's only north-south rail freight route, would be out of service.

"We cannot determine the full extent of the damage until we undertake a more detailed ground assessment," he said.

"We will only commence a ground investigation once having established that it is safe to do so."

That could be days, as the river's swelling continues under torrential rainfall.

More than 380mm of rain fell on the region on Monday, washing away sections of the Stuart Highway, cutting road access north of Katherine.

The Ghan passenger train was forced to stop in Katherine, leaving 200 passengers stranded and unable to continue their journey by rail or road.

The group spent last night night aboard the train in Katherine.

They will be found accommodation today and their travel will depend on the reopening of roads.

The freight train that derailed at the Edith River Crossing after flood waters washed away the tracks. Picture: Michael FranchiSource: Northern Territory News

The freight train that derailed at the Edith River Crossing after flood waters washed away the tracks. Picture: Michael FranchiSource: Northern Territory News

The Ghan's operator, Great Southern Rail, plans to send the train back to Adelaide with passengers who choose to return.

GSR spokeswoman Jessica Playford said the company had not been given any indication when the track would reopen.

"We're not sure when we'll be able to get through. I imagine not until the waters come down and they can actually have a look at what's happened."

Two train drivers aboard the GWA freight train were airlifted to Katherine for treatment of minor injuries and have since been flown to Darwin for more treatment.

NT Environment Department chief executive Jim Grant said copper concentrate "is recognised as an environmental hazard" and is a threat to aquatic life , but that although it contains arsenic and silica it is not rated as highly toxic.

Mr Grant said assessors yesterday took aerial shots of the site, which was not only cut off to the south by the Edith River, but also to the north by the Cullen River.

He said once it was safe to do so, they would take water and benthic samples (from the bottom of streams) for testing.

Mr Grant was unwilling to speculate how big the spill might be, or how difficult it would be to clean up, but that legal action could follow.

"When we do an investigation, prosecution is one of the possible outcomes ... everything I say could end up in court," he said.

"(But) it's serious enough to investigate very carefully."

GWA's Mr Easthope estimated the train was carrying 120 tonnes of copper concentrate, along with containers of consumables.

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